8YHZ | pdb_00008yhz

The co-crystal structure of the Fab fragment of Ab-1080 with NaV1.7 VSDII peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 
    0.210 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Intra-channel bi-epitopic crosslinking unleashes ultrapotent antibodies targeting Na V 1.7 for pain alleviation.

Zhang, Y.Ding, Y.Zeng, Z.Zhu, R.Zheng, P.Fan, S.Cao, Q.Chen, H.Ren, W.Wu, M.Wang, L.Du, J.

(2024) Cell Rep Med 5: 101800-101800

  • DOI: https://doi.org/10.1016/j.xcrm.2024.101800
  • Primary Citation of Related Structures:  
    8YHZ

  • PubMed Abstract: 

    Crucial for cell activities, ion channels are key drug discovery targets. Although small-molecule and peptide modulators dominate ion channel drug discovery, antibodies are emerging as an alternative modality. However, challenges persist in generating potent antibodies, especially for channels with limited extracellular epitopes. We herein present a bi-epitopic crosslinking strategy to overcome these challenges, focusing on Na V 1.7, a potential analgesic target. Aiming to crosslink two non-overlapping epitopes on voltage-sensing domains II and IV, we construct bispecific antibodies and ligand-antibody conjugates. Enhanced affinity and potency are observed in comparison to the monospecific controls. Among them, a ligand-antibody conjugate (1080-PEG 7 -ACDTB) displays a two-orders-of-magnitude improvement in potency (IC 50 of 0.06 ± 0.01 nM) and over 1,000-fold selectivity for Na V 1.7. Additionally, this conjugate demonstrates robust analgesic effects in mouse pain models. Our study introduces an approach to developing effective antibodies against Na V 1.7, thereby initiating a promising direction for the advancement of pain therapeutics.


  • Organizational Affiliation
    • School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China; Peking University-Tsinghua University-National Institute Biological Sciences (PTN) Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of 1080 FabA [auth L]218Oryctolagus cuniculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of 1080 FabB [auth H]214Oryctolagus cuniculusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel protein type 9 subunit alphaC [auth P]11Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15858 (Homo sapiens)
Explore Q15858 
Go to UniProtKB:  Q15858
PHAROS:  Q15858
GTEx:  ENSG00000169432 
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UniProt GroupQ15858
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free:  0.210 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.965α = 90
b = 78.965β = 90
c = 147.048γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82373774

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Database references, Structure summary
  • Version 1.2: 2024-12-04
    Changes: Database references